I've had problems several times this year. All with 'complications' in my record.

1) Bizarre issue checking into a flight with a KLM leg. It allowed me to checkin, but did not print the boarding pass for the KLM leg. However, when I went back later to reprint my boarding pass it was there!

2) Back in February the delta.com would not let me checkin at all for a leg from FCO to CDG. In fact, they couldn't find my record at all in the system. Luckily I had my ticket # with me. They found that and were able to check me in at the counter. (I also tried checking in on KLM.com and AF.com and with the Kiosks with the same results).

3) On the same February flight I still could not checkin online for my return leg from CDG to ATL. I was forced to go to the ticket purchase deck in CDG to pay additional taxes. Delta refused to collect them over the phone. Outright refused. I have to say that these problems have softened considerably with the roll out of the Diamond line. If Diamond is the only way to get proper customer service then Delta has a troubled future.

4) Problems checking in when using SWU's. Both times I had to call the diamond line to get it resolved. The first time, it was a quick let me take this comment off your record for the return and then I could check in. The agent then restored the comment that was preventing the checkin. The next time the agent had no clue how to fix it and told me I had to check in at the airport. I insisted this was not going to work for me. We broke the call with me a very unhappy diamond, and then she called me back 15-20 minutes later (at midnight mind you) to tell me she had figured it out and that I should now try to checkin. And voila it worked. On my return flight I had no problems checking in at all.

Last year, it wouldn't allow OLCI for any international flights but they have since fixed that by allowing the entry of passport info at OLCI.

I will give Delta credit for making it better, but clearly they have not ironed out the bugs.

For the OP -- I would start by getting a TSA redress # and giving it to Delta to load into your record. That may help you clear up your problem. Let us know if it works!